Conveniently I work in this space, but note the following is primarily my own personal opinion.

Primarily there's a few reasons I prefer Android Auto over native Android on the car:

1. Ever had a phone that's a few years old slow down in you? Now imagine you buy a car for $60k, and three years down the line the (already sluggish to begin with) Android interface is bogged down by updates and is barely usable. Imagine Spotify drops support for that version of Android Automotive. Android Auto puts all the infotainment into something the customer controls, and something external to the car so you are not dependent upon the OEM to do their own due diligence to ensure functionality and compatibility. If my phone slows down from age/wear/increased software demands, I go buy a new $400 phone. If my car's infotainment slows down I....buy a new car? (Looking at you GM)

2. Like I said it moves the infotainment to something in the customer's (and Google/Apple's) hand. OEMs do not want this. Auto makers want you locked into their proprietary Android skins for two reasons. First, making it more difficult to leave their specific company's ecosystem. They (will) build in their own apps that you'll start putting all your settings and private info on. Things like remembering a driver's preferred seating and mirror arrangement and auto-adjusting, so when your spouse buys a car you go "Oh well if we both have brand X, it'll be easier to drive each other's cars." Etc. Second, they want all of your data. Legitimately the industry is on fire right now figuring out how much consumer data we can scrape and use/sell with these systems. The Android Automotive stack in a car is 300% sending data back to the OEM of literally anything they are legally allowed to collect. Probably more, too. Plug in Android Auto from my phone and yeah they're still spying on me, but they don't have my Spotify login info or my specific apps used, they just have what the vehicle can directly measure (still a terrifying amount).

In your specific case with a third party head unit..go ham and use the stock interface if you want. Personally I'd still use Android Auto, to top off my phone and to access my local music library (I don't stream music), but a third party has a lot less interest in spying on you or locking you in the same way an OEM does.

Also out of curiosity, what head unit did you get? I've got a 2012 Cruze I've considered installing one of those on but I can almost never find anything that seems actually trustworthy.